2014 Publications

Amrine, D. H., Katherine C. H. ;. Swingley, Wesley D. ;. Ardell. (2014). TRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria. 10(2), e1003454. https://doi.org/10.1371/journal.pcbi.1003454
Aronson, M., Myla F. J. ;. La Sorte, Frank A. ;. Nilon, Charles H. ;. Katti, Madhusudan; Goddard, Mark A. ;. Lepczyk, Christopher A. ;. Warren, Paige S. ;. Williams, Nicholas S. G. ;. Cilliers, Sarel; Clarkson, Bruce; Dobbs, Cynnamon; Dolan, Rebecca; Hedblom, Marcus; Klotz, Stefan; Kooijmans, Jip Louwe; Kühn, Ingolf; MacGregor-Fors, Ian; McDonnell, Mark; Mörtberg, Ulla; Pyšek, Petr; Siebert, Stefan; Sushinsky, Jessica; Werner, Peter; Winter. (2014). A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers. 281(1780), 20133330. https://doi.org/10.1098/rspb.2013.3330
Aronson, B. others, Myla FJ; La Sorte, Frank A; Nilon, Charles H; Katti, Madhusudan; Goddard, Mark A; Lepczyk, Christopher A; Warren, Paige S; Williams, Nicholas SG; Cilliers, Sarel; Clarkson. (2014). A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers. 281(1780), 20133330.
Barton, S. P., Carl; Iliopoulos, Costas S. ;. Lee, Inbok; Mouchard, Laurent; Park, Kunsoo; Pissis. (2014). Extending alignments with k -mismatches and ℓ -gaps. 525, 80–88. https://doi.org/10.1016/j.tcs.2013.06.012
Belamkar, S. B., Vikas; Weeks, Nathan T; Bharti, Arvind K; Farmer, Andrew D; Graham, Michelle A; Cannon. (2014). Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. 15(1), 950. https://doi.org/10.1186/1471-2164-15-950
Brauer, S. C., Elizabeth K. ;. Singh, Dharmendra K. ;. Popescu. (2014). Next-generation plant science: Putting big data to work. 15(1), 301. https://doi.org/10.1186/gb4149
Brunbjerg, J.-C., A. K. ;. Cavender-Bares, J. ;. Eiserhardt, W. L. ;. Ejrnaes, R. ;. Aarssen, L. W. ;. Buckley, H. L. ;. Forey, E. ;. Jansen, F. ;. Kattge, J. ;. Lane, C. ;. Lubke, R. A. ;. Moles, A. T. ;. Monserrat, A. L. ;. Peet, R. K. ;. Roncal, J. ;. Wootton, L. ;. Svenning. (2014). Multi-scale phylogenetic structure in coastal dune plant communities across the globe. 7(2), 101–114. https://doi.org/10.1093/jpe/rtt069
Buckner, B. (2014, January 11). Introducing Genome Browsers, Genome Structure, and Gene Annotation.
Caciula, A. (2014). Optimization techniques for next-generation sequencing data analysis.
Campbell, M., Michael S. ;. Holt, Carson; Moore, Barry; Yandell. (2014a). Genome Annotation and Curation Using MAKER and MAKER-P: Genome Annotation and Curation Using MAKER and MAKER-P (J. R. Bateman Alex; Pearson, William R. ;. Stein, Lincoln D. ;. Stormo, Gary D. ;. Yates, Ed.; p. 4.11.1-4.11.39). http://doi.wiley.com/10.1002/0471250953.bi0411s48
Campbell, M., Michael S. ;. Law, MeiYee; Holt, Carson; Stein, Joshua C. ;. Moghe, Gaurav D. ;. Hufnagel, David E. ;. Lei, Jikai; Achawanantakun, Rujira; Jiao, Dian; Lawrence, Carolyn J. ;. Ware, Doreen; Shiu, Shin-Han; Childs, Kevin L. ;. Sun, Yanni; Jiang, Ning; Yandell. (2014b). MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations. 164(2), 513–524. https://doi.org/10.1104/pp.113.230144
Carnaby, S., Penny; Charters, Stuart; Staincliffe, Paul; Cahalane, Rosie; Laurenson, Matthew; Gibb, Robert; McGlinchy, Aaron; Sutherland. (2014). Lincoln Hub data and information architecture project: DATA$^2$: Data architecture transforming access & analysis.
Chalhoub, P., B. ;. Denoeud, F. ;. Liu, S. ;. Parkin, I. A. P. ;. Tang, H. ;. Wang, X. ;. Chiquet, J. ;. Belcram, H. ;. Tong, C. ;. Samans, B. ;. Correa, M. ;. Da Silva, C. ;. Just, J. ;. Falentin, C. ;. Koh, C. S. ;. Le Clainche, I. ;. Bernard, M. ;. Bento, P. ;. Noel, B. ;. Labadie, K. ;. Alberti, A. ;. Charles, M. ;. Arnaud, D. ;. Guo, H. ;. Daviaud, C. ;. Alamery, S. ;. Jabbari, K. ;. Zhao, M. ;. Edger, P. P. ;. Chelaifa, H. ;. Tack, D. ;. Lassalle, G. ;. Mestiri, I. ;. Schnel, N. ;. Le Paslier, M. C. ;. Fan, G. ;. Renault, V. ;. Bayer, P. E. ;. Golicz, A. A. ;. Manoli, S. ;. Lee, T. H. ;. Thi, V. H. D. ;. Chalabi, S. ;. Hu, Q. ;. Fan, C. ;. Tollenaere, R. ;. Lu, Y. ;. Battail, C. ;. Shen, J. ;. Sidebottom, C. H. D. ;. Wang, X. ;. Canaguier, A. ;. Chauveau, A. ;. Berard, A. ;. Deniot, G. ;. Guan, M. ;. Liu, Z. ;. Sun, F. ;. Lim, Y. P. ;. Lyons, E. ;. Town, C. D. ;. Bancroft, I. ;. Wang, X. ;. Meng, J. ;. Ma, J. ;. Pires, J. C. ;. King, G. J. ;. Brunel, D. ;. Delourme, R. ;. Renard, M. ;. Aury, J. M. ;. Adams, K. L. ;. Batley, J. ;. Snowdon, R. J. ;. Tost, J. ;. Edwards, D. ;. Zhou, Y. ;. Hua, W. ;. Sharpe, A. G. ;. Paterson, A. H. ;. Guan, C. ;. Wincker. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. 345(6199), 950–953. https://doi.org/10.1126/science.1253435
Chen, V. C. M., Min; Mao, Shiwen; Zhang, Yin; Leung. (2014). Big Data. http://link.springer.com/10.1007/978-3-319-06245-7
Chen, Y., Min; Mao, Shiwen; Liu. (2014). Big data: A survey. 19(2), 171–209.
Cholia, T., Shreyas; Sun. (2014). The NEWT Platform: An Extensible Plugin Framework for Creating ReSTful HPC APIs. 17–20. https://doi.org/10.1109/GCE.2014.14
Cuccuru, G., Gianmauro; Leo, Simone; Lianas, Luca; Muggiri, Michele; Pinna, Andrea; Pireddu, Luca; Uva, Paolo; Angius, Andrea; Fotia, Giorgio; Zanetti. (2014). An automated infrastructure to support high-throughput bioinformatics. 600–607. https://doi.org/10.1109/HPCSim.2014.6903742
Dahdul, M. A., Wasila M; Cui, Hong; Mabee, Paula M; Mungall, Christopher J; Osumi-Sutherland, David; Walls, Ramona L; Haendel. (2014). Nose to tail, roots to shoots: Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. 5(1), 34. https://doi.org/10.1186/2041-1480-5-34
Das, J. S., Abhiram; Bucksch, Alexander; Price, Charles A; Weitz. (2014). ClearedLeavesDB: an online database of cleared plant leaf images. 10(1), 8. https://doi.org/10.1186/1746-4811-10-8
Der, J. P. (2014, January 14). A unified global gene family classification resource for plants and its utility for comparative genomics, genome annotation, and gene family studies.
Dooley, J., Rion; Stubbs. (2014). Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave. 2-Jan. https://doi.org/10.1145/2616498.2616561
Duvick, J. (2014, January 14). Genome annotation in the cloud through xGDBvm virtual server instances deployed at iPlant.
Esa. (2014). The 2014 Annual Reports to the Governing Council: ESA 99 th Annual Meeting, Sacramento, California, August 9 th -15 th , 2014. 95(4), S1–S69. https://doi.org/10.1890/2014.councilreport
Feltus, F. A. (2014). Systems genetics: A paradigm to improve discovery of candidate genes and mechanisms underlying complex traits. 223, 45–48. https://doi.org/10.1016/j.plantsci.2014.03.003
Gardiner, A., Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall. (2014). Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species. 80(5), 895–904. https://doi.org/10.1111/tpj.12660
Gehring, T. G., Catherine; Flores-Rentería, Dulce; Sthultz, Christopher M. ;. Leonard, Tierra M. ;. Flores-Rentería, Lluvia; Whipple, Amy V. ;. Whitham. (2014). Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change. 23(6), 1379–1391. https://doi.org/10.1111/mec.12503
Gnimpieba, C. M., Etienne Z. ;. Chango, Abalo; Lushbough. (2014). RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative. 661–669. https://doi.org/10.1145/2649387.2660822
Goodrich, R. E., Julia K. ;. Di Rienzi, Sara C. ;. Poole, Angela C. ;. Koren, Omry; Walters, William A. ;. Caporaso, J. Gregory; Knight, Rob; Ley. (2014). Conducting a Microbiome Study. 158(2), 250–262. https://doi.org/10.1016/j.cell.2014.06.037
Gorton, I. (2014). Cyberinfrastructures: Bridging the Divide between Scientific Research and Software Engineering. 47(8), 48–55. https://doi.org/10.1109/MC.2013.336
Hanlon, E., Matthew R; Vaughn, Matthew; Mock, Stephen; Dooley, Rion; Moreira, Walter; Stubbs, Joe; Town, Chris; Miller, Jason; Krishnakumar, Vivek; Ferlanti, Erik; Pence. (2014). The Arabidopsis Information Portal: An Application Platform for Data Discovery. 38–41. https://doi.org/10.1109/GCE.2014.10
Hanssen, A. M., F. ;. Heggberget, T. ;. Bladt, J. ;. Endresen, D. ;. Forsius, M. ;. Gudmundsson, G. ;. Gärdenfors, U. ;. Heiðmarsson, S. ;. Kindvall, O. ;. Koch, W. ;. Koviula, K. ;. Laiho, E. L. ;. Laine, K. ;. Obst, M. ;. Skov, F. ;. Telenius, A. ;. Vallan, N. ;. Wasowicz, P. ;. Wremp. (2014). Nordic LifeWatch Cooperation. Final report.
Hart, M., David L. ;. Schuele, Amy; Soriano, Ester; Dahan, Maytal; Hanlon. (2014). XRAS: Allocations software as a service in XSEDE. 8-Jan. https://doi.org/10.1145/2616498.2616562
Hilgert, D., Uwe; McKay, Sheldon; Khalfan, Mohammed; Williams, Jason; Ghiban, Cornel; Micklos. (2014). DNA Subway: Making Genome Analysis Egalitarian. 3-Jan. https://doi.org/10.1145/2616498.2616575
Holmgren, J. L., Camille A. ;. Betancourt, Julio L. ;. Peñalba, M. Cristina; Delgadillo, José; Zuravnsky, Kristin; Hunter, Kimberly L. ;. Rylander, Kate A. ;. Weiss. (2014). Evidence against a Pleistocene desert refugium in the Lower Colorado River Basin. 41(9), 1769–1780. https://doi.org/10.1111/jbi.12337
Horvath, D. J. V. A. M. D. B. S. (2014, January 14). Progress in Sequencing the Genome of an Invasive Polyploid Weed (Leafy Spurge).
Huang, E. A., Pu; Feldman, Maximilian; Schroder, Stephan; Bahri, Bochra A. ;. Diao, Xianmin; Zhi, Hui; Estep, Matt; Baxter, Ivan; Devos, Katrien M. ;. Kellogg. (2014). Population genetics of Setaria viridis , a new model system. 23(20), 4912–4925. https://doi.org/10.1111/mec.12907
Hurwitz, B. (2014, January 14). iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant Cyberinfrastructure.
Hurwitz, M. B., B. L. ;. Westveld, A. H. ;. Brum, J. R. ;. Sullivan. (2014). Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. 111(29), 10714–10719. https://doi.org/10.1073/pnas.1319778111
Ichihashi, N. R., Y. ;. Aguilar-Martinez, J. A. ;. Farhi, M. ;. Chitwood, D. H. ;. Kumar, R. ;. Millon, L. V. ;. Peng, J. ;. Maloof, J. N. ;. Sinha. (2014). Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. 111(25), E2616–E2621. https://doi.org/10.1073/pnas.1402835111
Izquierdo-Carrasco, A., Fernando; Cazes, John; Smith, Stephen A; Stamatakis. (2014). PUmPER: phylogenies updated perpetually. 30(10), 1476–1477.
Jamann, R. J., Tiffany M. ;. Poland, Jesse A. ;. Kolkman, Judith M. ;. Smith, Laurie G. ;. Nelson. (2014). Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize. 198(1), 333–344. https://doi.org/10.1534/genetics.114.167486
Jazayeri, H. M., Seyed Mehdi; Melgarejo-Muñoz, Luz Marina; Romero. (2014). RNA-SEQ: A GLANCE AT TECHNOLOGIES AND METHODOLOGIES. 20(2). https://doi.org/10.15446/abc.v20n2.43639
Kanewala, M., Thejaka Amila; Marru, Suresh; Basney, Jim; Pierce. (2014). A Credential Store for Multi-tenant Science Gateways. 445–454. https://doi.org/10.1109/CCGrid.2014.95
Katz, C., Daniel S. ;. Choi, Sou-Cheng T. ;. Lapp, Hilmar; Maheshwari, Ketan; Löffler, Frank; Turk, Matthew; Hanwell, Marcus D. ;. Wilkins-Diehr, Nancy; Hetherington, James; Howison, James; Swenson, Shel; Allen, Gabrielle D. ;. Elster, Anne C. ;. Berriman, Bruce; Venters. (2014). Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1). 2(1), e6. https://doi.org/10.5334/jors.an
Kim, J. H., G. ;. LeBlanc, M. L. ;. Wafula, E. K. ;. dePamphilis, C. W. ;. Westwood. (2014). Genomic-scale exchange of mRNA between a parasitic plant and its hosts. 345(6198), 808–811. https://doi.org/10.1126/science.1253122
Koesterke, D., Lars; Koltes, James E. ;. Weeks, Nathan T. ;. Milfeld, Kent; Vaughn, Matthew W. ;. Reecy, James M. ;. Stanzione. (2014). Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede’s Xeon and Xeon Phi processors: ACCELERATED BIOLOGICAL NETWORK DISCOVERY WITH PCIT. 26(13), 2178–2190. https://doi.org/10.1002/cpe.3252
Lammers, B., Youri; Peelen, Tamara; Vos, Rutger A; Gravendeel. (2014). The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. 15(1), 44. https://doi.org/10.1186/1471-2105-15-44
Lawrence, S., Katherine A. ;. Wilkins-Diehr, Nancy; Wernert, Julie A. ;. Pierce, Marlon; Zentner, Michael; Marru. (2014). Who Cares about Science Gateways? A Large-Scale Survey of Community Use and Needs. 4-Jan. https://doi.org/10.1109/GCE.2014.11
LeDuc, W., Richard; Vaughn, Matthew; Fonner, John M; Sullivan, Michael; Williams, James G; Blood, Philip D; Taylor, James; Barnett. (2014). Leveraging the national cyberinfrastructure for biomedical research. 21(2), 195–199. https://doi.org/10.1136/amiajnl-2013-002059
Li, H. H. Y. W. T.-S. C. X. (2014). Toward Scalable Systems for Big Data Analytics: A Technology Tutorial. 2, 652–687. https://doi.org/10.1109/ACCESS.2014.2332453
Ma, X., Chuang; Zhang, Hao Helen; Wang. (2014). Machine learning for Big Data analytics in plants. 19(12), 798–808. https://doi.org/10.1016/j.tplants.2014.08.004
Maia, D. E., Vitor H; Gitzendanner, Matthew A; Soltis, Pamela S; Wong, Gane Ka-Shu; Soltis. (2014). Angiosperm phylogeny based on 18S/26S rDNA sequence data: Constructing a large data set using next-generation sequence data. 175(6), 613–650.
Makinde, D. (2014). African Orphan Crops Consortium: A NEPAD-led initiative. 57.
Mandadi, K. K. K.-B. G. S. (2014, January 14). Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic Virus.
Matasci, G. K.-S., Naim; Hung, Ling-Hong; Yan, Zhixiang; Carpenter, Eric J; Wickett, Norman J; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Ayyampalayam, Saravanaraj; Barker, Michael; Burleigh, J. Gordon; Gitzendanner, Matthew A; Wafula, Eric; Der, Joshua P; dePamphilis, Claude W; Roure, Béatrice; Philippe, Hervé; Ruhfel, Brad R; Miles, Nicholas W; Graham, Sean W; Mathews, Sarah; Surek, Barbara; Melkonian, Michael; Soltis, Douglas E; Soltis, Pamela S; Rothfels, Carl; Pokorny, Lisa; Shaw, Jonathan A; DeGironimo, Lisa; Stevenson, Dennis W; Villarreal, Juan Carlos; Chen, Tao; Kutchan, Toni M; Rolf, Megan; Baucom, Regina S; Deyholos, Michael K; Samudrala, Ram; Tian, Zhijian; Wu, Xiaolei; Sun, Xiao; Zhang, Yong; Wang, Jun; Leebens-Mack, Jim; Wong. (2014). Data access for the 1,000 Plants (1KP) project. 3(1), 17. https://doi.org/10.1186/2047-217X-3-17
Melicher, J. H., Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher. (2014). A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. 15(1), 188. https://doi.org/10.1186/1471-2164-15-188
Mentewab, B., Ayalew; Matheson, Kinnari; Adebiyi, Morayo; Robinson, Shanice; Elston. (2014). RNA-seq analysis of the effect of kanamycin and the ABC transporter AtWBC19 on Arabidopsis thaliana seedlings reveals changes in metal content. 9(10), e109310.
Merelli, D., Ivan; Pérez-Sánchez, Horacio; Gesing, Sandra; D’Agostino. (2014a). High-Performance Computing and Big Data in Omics-Based Medicine. 2014, 2-Jan. https://doi.org/10.1155/2014/825649
Merelli, D., Ivan; Pérez-Sánchez, Horacio; Gesing, Sandra; D’Agostino. (2014b). Managing, analysing, and integrating big data in medical bioinformatics: Open problems and future perspectives. 2014.
Michaletz, B. J., Sean T. ;. Cheng, Dongliang; Kerkhoff, Andrew J. ;. Enquist. (2014). Convergence of terrestrial plant production across global climate gradients. 512(7512), 39–43. https://doi.org/10.1038/nature13470
Micklos, D. (2014, January 11). A Simple Bioinformatics Workflow for RNA-Seq Analysis and Distributed Genome Annotation.
Minervini, S. A., Massimo; Abdelsamea, Mohammed M. ;. Tsaftaris. (2014). Image-based plant phenotyping with incremental learning and active contours. 23, 35–48. https://doi.org/10.1016/j.ecoinf.2013.07.004
Mirarab, T., S. ;. Reaz, R. ;. Bayzid, Md. S. ;. Zimmermann, T. ;. Swenson, M. S. ;. Warnow. (2014a). ASTRAL: genome-scale coalescent-based species tree estimation. 30(17), i541–i548. https://doi.org/10.1093/bioinformatics/btu462
Mirarab, T., Siavash; Bayzid, Md Shamsuzzoha; Boussau, Bastien; Warnow. (2014b). Avian Model Species Trees for 1X Model Condition for Mirarab et. Al.
Mirarab, T., Siavash; Bayzid, Md Shamsuzzoha; Boussau, Bastien; Warnow. (2014c). Bin Definition for Super Gene Trees for Mirarab et. Al.
Mirarab, T., Siavash; Bayzid, Md Shamsuzzoha; Boussau, Bastien; Warnow. (2014d). Binning Code for Mirarab et. Al.
Mirarab, T., Siavash; Bayzid, Md Shamsuzzoha; Boussau, Bastien; Warnow. (2014e). Sequence Alignments and Trees for Avian 1X for Mirarab et. Al.
Mirarab, T., Siavash; Nguyen, Nam; Warnow. (2014f). PASTA: ultra-large multiple sequence alignment. 177–191.
Mohan, T., Anup; Hacker, Thomas; Rodgers, Gregory P. ;. Islam. (2014). Batchsubmit: A high-volume batch submission system for earthquake engineering simulation: BATCHSUBMIT: A HIGH-VOLUME BATCH SUBMISSION SYSTEM. 26(13), 2240–2252. https://doi.org/10.1002/cpe.3234
Nezhad, A. S. (2014). Future of portable devices for plant pathogen diagnosis. 14(16), 2887–2904. https://doi.org/10.1039/C4LC00487F
Ningthoujam, A. D., Sanjoy Singh; Choudhury, Manabendra Dutta; Potsangbam, Kumar Singh; Chetia, Pankaj; Nahar, Lutfun; Sarker, Satyajit D. ;. Basar, Norazah; Talukdar. (2014). NoSQL Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources: NoSQL Data Model for Integration of Ethnomedicinal Plant Data. 25(6), 495–507. https://doi.org/10.1002/pca.2520
Numa, T., H. ;. Itoh. (2014). MEGANTE: A Web-Based System for Integrated Plant Genome Annotation. 55(1), e2–e2. https://doi.org/10.1093/pcp/pct157
Oaks, J., Jamie R. ;. Linkem, Charles W. ;. Sukumaran. (2014). Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al. 68(12), 3607–3617. https://doi.org/10.1111/evo.12523
Oaks, J. R. (2014). An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History. 14(1), 150. https://doi.org/10.1186/1471-2148-14-150
Parr, R., Cynthia S. ;. Wilson, Nathan; Leary, Patrick; Schulz, Katja; Lans, Kristen; Walley, Lisa; Hammock, Jennifer; Goddard, Anthony; Rice, Jeremy; Studer, Marie; Holmes, Jeffrey; Corrigan, Jr. (2014). The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth. 2, e1079. https://doi.org/10.3897/BDJ.2.e1079
Parry, G. (2014). Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth. 65(20), 6057–6067. https://doi.org/10.1093/jxb/eru346
Poelchau, P., Monica F. ;. Huang, Xin; Goff, Allison; Reynolds, Julie; Armbruster. (2014). An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus. 93, 51961. https://doi.org/10.3791/51961
Rajasekar, Arcot. (2014). The Librarian & the Big Data: Bridging the Gap.
Rajasekar, R., Arcot; Xu, Hao; Moore. (2014). Note on Three Classes of Data Grid Operations. 2(6), 6-Jan. https://doi.org/10.4236/jcc.2014.26001
Ranjan, N. R., A. ;. Ichihashi, Y. ;. Farhi, M. ;. Zumstein, K. ;. Townsley, B. ;. David-Schwartz, R. ;. Sinha. (2014). De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism. 166(3), 1186–1199. https://doi.org/10.1104/pp.113.234864
Reecy, J. C. B. E. F.-W. J. E. K. M. D. B. B. C. F. H. S.-H. C. S. R. L. F. D. J. Garrick. ; F. S.-H. B. G. M. V. (2014). Computational resources to facilitate variant discovery and analysis. 23.
Reecy, J. ; J. P. C. F. M. J. E. K. E. F.-W. J. W. E. L. C. F. B. M. W. V. (2014). Cyberinfrastructure for Life Sciences—IAnimal resources for genomics and other data driven biology. 9911.
Rees, T. (2014). Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases. 9(9), e107510. https://doi.org/10.1371/journal.pone.0107510
Rhee, M., Seung Yon; Mutwil. (2014). Towards revealing the functions of all genes in plants. 19(4), 212–221. https://doi.org/10.1016/j.tplants.2013.10.006
Robinson, R. P., Natalie; Regetz, James; Guralnick. (2014). EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM data. 87, 57–67. https://doi.org/10.1016/j.isprsjprs.2013.11.002
Ruhfel, J., Brad R; Gitzendanner, Matthew A; Soltis, Pamela S; Soltis, Douglas E; Burleigh. (2014). From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. 14(1), 23. https://doi.org/10.1186/1471-2148-14-23
Sachdeva, B., Paramjit S; Edmeades, Gregory O; Mumm, Rita H; Rafalski, Antoni J; Bennett. (2014). Report of the final external review of the Generation Challenge Programme.
Schatz, W. R., Michael C; Maron, Lyza G; Stein, Joshua C; Hernandez Wences, Alejandro; Gurtowski, James; Biggers, Eric; Lee, Hayan; Kramer, Melissa; Antonio, Eric; Ghiban, Elena; Wright, Mark H; Chia, Jer-ming; Ware, Doreen; McCouch, Susan R; McCombie. (2014). New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica. http://biorxiv.org/lookup/doi/10.1101/003764
Scott, T. (2014). Identification of GCN4 homologues in maize using a bioinformatics approach.
Shaffer, S. C. R., Christopher D. ;. Alvarez, Consuelo J. ;. Bednarski, April E. ;. Dunbar, David; Goodman, Anya L. ;. Reinke, Catherine; Rosenwald, Anne G. ;. Wolyniak, Michael J. ;. Bailey, Cheryl; Barnard, Daron; Bazinet, Christopher; Beach, Dale L. ;. Bedard, James E. J. ;. Bhalla, Satish; Braverman, John; Burg, Martin; Chandrasekaran, Vidya; Chung, Hui-Min; Clase, Kari; DeJong, Randall J. ;. DiAngelo, Justin R. ;. Du, Chunguang; Eckdahl, Todd T. ;. Eisler, Heather; Emerson, Julia A. ;. Frary, Amy; Frohlich, Donald; Gosser, Yuying; Govind, Shubha; Haberman, Adam; Hark, Amy T. ;. Hauser, Charles; Hoogewerf, Arlene; Hoopes, Laura L. M. ;. Howell, Carina E. ;. Johnson, Diana; Jones, Christopher J. ;. Kadlec, Lisa; Kaehler, Marian; Silver Key, S. Catherine; Kleinschmit, Adam; Kokan, Nighat P. ;. Kopp, Olga; Kuleck, Gary; Leatherman, Judith; Lopilato, Jane; MacKinnon, Christy; Martinez-Cruzado, Juan Carlos; McNeil, Gerard; Mel, Stephanie; Mistry, Hemlata; Nagengast, Alexis; Overvoorde, Paul; Paetkau, Don W. ;. Parrish, Susan; Peterson, Celeste N. ;. Preuss, Mary; Reed, Laura K. ;. Revie, Dennis; Robic, Srebrenka; Roecklein-Canfield, Jennifer; Rubin, Michael R. ;. Saville, Kenneth; Schroeder, Stephanie; Sharif, Karim; Shaw, Mary; Skuse, Gary; Smith, Christopher D. ;. Smith, Mary A. ;. Smith, Sheryl T. ;. Spana, Eric; Spratt, Mary; Sreenivasan, Aparna; Stamm, Joyce; Szauter, Paul; Thompson, Jeffrey S. ;. Wawersik, Matthew; Youngblom, James; Zhou, Leming; Mardis, Elaine R. ;. Buhler, Jeremy; Leung, Wilson; Lopatto, David; Elgin. (2014). A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time. 13(1), 111–130. https://doi.org/10.1187/cbe-13-08-0152
Smith, T. L., Halie C; Niewohner, Devon J; Dewey, Grant D; Longo, Autumn M; Guy, Tracy L; Higgins, Bradley R; Daehling, Sarah B; Genrich, Sarah C. ;. Wentworth, Christopher D; Durham Brooks. (2014). Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response. 83, 50878. https://doi.org/10.3791/50878
Snoderly-Foster, L. (2014). Characterization of a plant gene family expanded in glycine max.
Soderlund, S. A., Carol A. ;. Nelson, William M. ;. Goff. (2014). Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression. 9(12), e115740. https://doi.org/10.1371/journal.pone.0115740
Staff, T. P. O. (2014). Correction: De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. 9(8), e105275. https://doi.org/10.1371/journal.pone.0105275
Stewart, C. A. (2014). Serving national scientific communities: Genome analysis as an example.
Stobbe, U., A. H. ;. Schneider, W. L. ;. Hoyt, P. R. ;. Melcher. (2014). Screening Metagenomic Data for Viruses Using the E-Probe Diagnostic Nucleic Acid Assay. 104(10), 1125–1129. https://doi.org/10.1094/PHYTO-11-13-0310-R
Thavappiragasam, E. Z., Mathialakan; Lushbough, Carol M. ;. Gnimpieba. (2014a). Heuristic parallelizable algorithm for similarity based biosystems comparison. 782–789. https://doi.org/10.1145/2649387.2660849
Thavappiragasam, E. Z., Mathialakan; Lushbough, Carol M; Gnimpieba. (2014b). SBMLChecker, a Semantic approach for SBML model reliability evaluation. 1.
Tong, X., Qiuhui; Yuan, Bo; Li. (2014). Cyberinfrastructure: Applications and challenges. 74–80.
Towns, N., John; Cockerill, Timothy; Dahan, Maytal; Foster, Ian; Gaither, Kelly; Grimshaw, Andrew; Hazlewood, Victor; Lathrop, Scott; Lifka, Dave; Peterson, Gregory D. ;. Roskies, Ralph; Scott, J. Ray; Wilkins-Diehr. (2014). XSEDE: Accelerating Scientific Discovery. 16(5), 62–74. https://doi.org/10.1109/MCSE.2014.80
Tukamuhabwa, L. A. (2014). Application of Bioinformatics in Crop Improvement: Annotating the Putative Soybean Rust resistance gene Rpp3 for Enhancing Marker Assisted Selection. 7(1). https://doi.org/10.4172/jpb.1000296
Uribe-Convers, D. C., Simon; Duke, Justin R. ;. Moore, Michael J. ;. Tank. (2014). A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies. 2(1), 1300063. https://doi.org/10.3732/apps.1300063
Van Gorp, L., Pieter; Rose. (2014). Guest editors’ introduction to the first issue on Experimental Software Engineering in the Cloud (ESEiC). 85, 4-Jan. https://doi.org/10.1016/j.scico.2013.12.007
Vasquez-Gross, H. J. Z. D. G. D. N. J. W. (2014, January 14). Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP.
Vaughn, M. (2014, January 13). The Arabidopsis Information Portal: A First Glimpse.
Verborgh, R., Ruben; Harth, Andreas; Maleshkova, Maria; Stadtmüller, Steffen; Steiner, Thomas; Taheriyan, Mohsen; Van de Walle. (2014). Survey of Semantic Description of REST APIs (R. Pautasso Cesare; Wilde, Erik; Alarcon, Ed.; pp. 69–89). http://link.springer.com/10.1007/978-1-4614-9299-3_5
Walls, J., Ramona L. ;. Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Tuama, Éamonn Ó. ;. Schildhauer, Mark; Smith, Barry; Stucky, Brian J. ;. Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley. (2014). Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. 9(3), e89606. https://doi.org/10.1371/journal.pone.0089606
Walls, J., Ramona L; Guralnick, Robert; Deck, John; Buntzman, Adam; Buttigieg, Pier Luigi; Davies, Neil; Denslow, Michael W; Gallery, Rachel E; Parnell, J. Jacob; Osumi-Sutherland, David; Robbins, Robert J; Rocca-Serra, Philippe; Wieczorek, John; Zheng. (2014). Meeting report: Advancing practical applications of biodiversity ontologies. 9(1), 17. https://doi.org/10.1186/1944-3277-9-17
Walls, R. J. D. R. G. A. M. (2014). A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections. http://ceur-ws.org/Vol-1309/paper8.pdf
Wang, D., Liya; Stein, Lincoln; Ware. (2014). The relationships among GC content, nucleosome occupancy, and exon size. http://arxiv.org/abs/1404.2487
Wang, L., Liya; Ware, Doreen; Lushbough, Carol; Merchant, Nirav; Stein. (2014). A GWAS platform built on iPlant cyber-infrastructure. http://biorxiv.org/lookup/doi/10.1101/002881
Wang, P., Fusheng; Niedermayr, Cristobal Vergara; Liu. (2014). Metadata based management and sharing of distributed biomedical data. 9(1), 42. https://doi.org/10.1504/IJMSO.2014.059126
Weinandt, C., Nick; Jackson, Laura M. ;. Gnimpieba, Etienne Z. ;. Lushbough. (2014). Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison. 797–804. https://doi.org/10.1145/2649387.2660851
Werner, E. T., Gijsbert D. A. ;. Cornwell, William K. ;. Sprent, Janet I. ;. Kattge, Jens; Kiers. (2014). A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. 5(1), 4087. https://doi.org/10.1038/ncomms5087
West, N. M., Patrick T. ;. Li, Qing; Ji, Lexiang; Eichten, Steven R. ;. Song, Jawon; Vaughn, Matthew W. ;. Schmitz, Robert J. ;. Springer. (2014). Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome. 9(8), e105267. https://doi.org/10.1371/journal.pone.0105267
Wickett, J., Norman J. ;. Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Carpenter, Eric; Matasci, Naim; Ayyampalayam, Saravanaraj; Barker, Michael S. ;. Burleigh, J. Gordon; Gitzendanner, Matthew A. ;. Ruhfel, Brad R. ;. Wafula, Eric; Der, Joshua P. ;. Graham, Sean W. ;. Mathews, Sarah; Melkonian, Michael; Soltis, Douglas E. ;. Soltis, Pamela S. ;. Miles, Nicholas W. ;. Rothfels, Carl J. ;. Pokorny, Lisa; Shaw, A. Jonathan; DeGironimo, Lisa; Stevenson, Dennis W. ;. Surek, Barbara; Villarreal, Juan Carlos; Roure, Béatrice; Philippe, Hervé; dePamphilis, Claude W. ;. Chen, Tao; Deyholos, Michael K. ;. Baucom, Regina S. ;. Kutchan, Toni M. ;. Augustin, Megan M. ;. Wang, Jun; Zhang, Yong; Tian, Zhijian; Yan, Zhixiang; Wu, Xiaolei; Sun, Xiao; Wong, Gane Ka-Shu; Leebens-Mack. (2014). Phylotranscriptomic analysis of the origin and early diversification of land plants. 111(45), E4859–E4868. https://doi.org/10.1073/pnas.1323926111
Williams, D., J; McKay, S; Khalfan, M; Ghiban, C; Hilgert, U; Lauter, S; Jeong, ES; Micklos. (2014). DNA Subway–An educational bioinformatics platform for gene and genome analysis: DNA barcoding, and RNA-Seq.
Wilson, W., Adam M. ;. Parmentier, Benoit; Jetz. (2014). Systematic land cover bias in Collection 5 MODIS cloud mask and derived products—A global overview. 141, 149–154. https://doi.org/10.1016/j.rse.2013.10.025
Wilson-Sánchez, J. L., David; Rubio-Díaz, Silvia; Muñoz-Viana, Rafael; Pérez-Pérez, José Manuel; Jover-Gil, Sara; Ponce, María Rosa; Micol. (2014). Leaf phenomics: A systematic reverse genetic screen for Arabidopsis leaf mutants. 79(5), 878–891. https://doi.org/10.1111/tpj.12595
Wofford, A., Austin M. ;. Finch, Kristen; Bigott, Adam; Willyard. (2014). A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae). 2(5), 1400002. https://doi.org/10.3732/apps.1400002
Xu, D. (2014, January 14). Soybean knowledge base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding.
Xu, R., Hao; Ward, Jewel H. ;. Conway, Mike; Rajasekar, Arcot; Moore. (2014). Building an extensible file system via policy-based data management. 18-Nov. https://doi.org/10.1145/2603941.2603943
Zhao, L. E., Kangmei; Bartley. (2014). Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. 14(1), 135. https://doi.org/10.1186/1471-2229-14-135